Scientific Software
Updated 6 months ago

anndata — Peer-reviewed • Rank 24.6 • Science 95%

anndata: Access and store annotated data matrices - Published in JOSS (2024)

Engineering (40%)
Scientific Software · Peer-reviewed
Scientific Software
Updated 6 months ago

starfish — Peer-reviewed • Rank 17.4 • Science 95%

starfish: scalable pipelines for image-based transcriptomics - Published in JOSS (2021)

Engineering (40%)
Scientific Software · Peer-reviewed
Updated 6 months ago

unitvelo • Rank 9.2 • Science 67%

UniTVelo, Temporally Unified RNA Velocity for single cell trajectory inference

Updated 6 months ago

cosmosR • Rank 15.7 • Science 59%

COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets.

Updated 5 months ago

https://github.com/alleninstitute/scrattch • Rank 5.5 • Science 67%

Single cell RNA-seq analysis for transcriptomic type characterization

Updated 6 months ago

gemma.R • Rank 14.2 • Science 57%

An R wrapper for the Gemma RESTful API

Updated 6 months ago

mtp-db • Rank 2.1 • Science 67%

The Membrane Transport Protein Database

Updated 6 months ago

DIscBIO • Rank 14.5 • Science 54%

A user-friendly R pipeline for biomarker discovery in single-cell transcriptomics

Updated 6 months ago

macrophage-regulation • Rank 1.1 • Science 67%

Integrated time-series analysis and high-content CRISPR screening delineate the dynamics of macrophage immune regulation

Updated 6 months ago

cellxgene • Rank 17.9 • Science 46%

An interactive explorer for single-cell transcriptomics data

Updated 6 months ago

spatialvi • Rank 6.8 • Science 57%

Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.

Updated 6 months ago

molkart • Rank 4.5 • Science 57%

A pipeline for processing Molecular Cartography data from Resolve Bioscience (combinatorial FISH)

Updated 5 months ago

https://github.com/alleninstitute/scrattch.hicat • Rank 7.4 • Science 54%

Hierarchical, iterative clustering for analysis of transcriptomics data in R

Updated 5 months ago

https://github.com/alleninstitute/tasic2016data • Rank 3.3 • Science 54%

Single cell transcriptomic data from Tasic, et al. (2016)

Updated 6 months ago

iSEE • Rank 19.0 • Science 36%

R/shiny interface for interactive visualization of data in SummarizedExperiment objects

Updated 6 months ago

EWCE • Rank 16.4 • Science 36%

Expression Weighted Celltype Enrichment. See the package website for up-to-date instructions on usage.

Updated 6 months ago

pagoda2 • Rank 15.4 • Science 36%

R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets

Updated 6 months ago

cluefish • Rank 2.3 • Science 49%

A specialised workflow designed to enhance the biological interpretation of transcriptomic data series 🎣

Updated 6 months ago

fishpond • Rank 16.4 • Science 33%

Differential expression and allelic analysis, nonparametric statistics

Updated 6 months ago

scCATCH • Rank 14.0 • Science 33%

Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data

Updated 6 months ago

pyscenic • Rank 18.0 • Science 26%

pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.

Updated 6 months ago

curare • Rank 7.7 • Science 36%

Curare - A customizable and reproducible analysis pipeline for RNA-Seq experiments

Updated 5 months ago

https://github.com/cran-task-views/omics • Rank 5.0 • Science 36%

CRAN Task View: Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Updated 6 months ago

getDEE2 • Rank 11.5 • Science 26%

Programmatic access to the DEE2 RNA expression dataset.

Updated 6 months ago

icetea • Rank 12.7 • Science 20%

R/Bioconductor package for analysis of single and paired-end capped-RNAseq data (CAGE/RAMPAGE/MAPCap)

Updated 6 months ago

ODER • Rank 8.7 • Science 23%

Optimising Definitions of Expressed Regions

Updated 6 months ago

imsig • Rank 13.3 • Science 13%

Immune Cell Gene Signatures for Profiling the Microenvironment of Solid Tumours

Updated 5 months ago

https://github.com/bayer-group/cellenium • Rank 5.4 • Science 13%

Cellenium is a FAIR and scalable interactive visual analytics app for scRNA-Seq data (single-cell RNA sequencing).

Updated 5 months ago

https://github.com/alleninstitute/scrattch.io • Rank 4.2 • Science 10%

Functions for handling RNA-seq files and formats as input and output for scrattch functions.

Updated 6 months ago

singleCellHaystack • Science 26%

Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).

Updated 6 months ago

isocomp • Science 31%

Isocomp provides tools to compare any number of transcriptome assemblies (GTF + fasta) from long read RNAseq

Updated 6 months ago

tfactivity • Science 67%

Bioinformatics pipeline that makes use of expression and open chromatin data to identify differentially active transcription factors across conditions.

Updated 6 months ago

drugfindr • Science 36%

Repository holding the code for the drugfindR R package

Updated 6 months ago

SeedMatchR • Science 23%

Off-target analysis of siRNA knock down paired with RNAseq

Updated 5 months ago

https://github.com/broadinstitute/temporal-rna-seq-deconvolution • Science 26%

Package for temporal deconvolution of bulk RNA-seq samples using SVI

Updated 5 months ago

https://github.com/alleninstitute/lowcat • Science 13%

Low coverage accessibility and transcriptomics

Updated 6 months ago

bd-lithium • Science 54%

A collection of source codes for network-based multi-omics analysis using integrated genome-wide association studies (GWAS) and transcriptomic data to identify genetic contribution into lithium response in patients with bipolar disorder (BD).

Updated 6 months ago

rich_directrna • Science 57%

Nanopore directRNA (hopefully cDNA too ;)) workflow with many transcript reconstruction alternatives